Merge pull request #167 from pycroscopy/use_dict3

python 13 support for pypi

.github/workflows/actions.yml

@@ -1,7 +1,8 @@
 name: build
 
 env:
-  PYTHON_MAIN_VERSION: 3.9
+
+  PYTHON_MAIN_VERSION: 3.12
 
 on:
   pull_request:
@@ -19,7 +20,8 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python-version: ['3.9', '3.11', '3.12']
+
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v3
@@ -73,6 +75,6 @@ jobs:
       env: 
         PYPI_TOKEN_PASSWORD: ${{ secrets.API_TOKEN_PYPI2 }}
       run: |
-        pip install wheel twine
-        python setup.py sdist bdist_wheel
+        pip install wheel twine, build
+        python -m build --sdist --wheel
         twine upload --username "__token__" --password $PYPI_TOKEN_PASSWORD dist/*

.gitignore

@@ -252,3 +252,5 @@ _autosummary/pyTEMlib.version.rst
 _autosummary/pyTEMlib.xrpa_x_sections.rst
 notebooks/Imaging/Adaptive_Fourier_Filter-Copy1.ipynb
 notebooks/Spectroscopy/EELS_286.hf5
+notebooks/Spectroscopy/Untitled1.ipynb
+pyTEMlib/info_widget2.py

notebooks/Spectroscopy/Analyse_Low_Loss.ipynb

@@ -78,6 +78,7 @@
      "output_type": "stream",
      "text": [
       "installing pyTEMlib\n",
+      "^C\n",
       "done\n"
      ]
     }
@@ -134,7 +135,7 @@
       "You don't have gwyfile installed.     If you wish to open .gwy files, you will need to      install it (pip install gwyfile) before attempting.\n",
       "Symmetry functions of spglib enabled\n",
       "Using kinematic_scattering library version {_version_ }  by G.Duscher\n",
-      "pyTEM version:  0.2024.05.0\n"
+      "pyTEM version:  0.2024.06.1\n"
      ]
     }
    ],
@@ -184,18 +185,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {
     "hideCode": false,
     "hidePrompt": false,
-    "scrolled": true,
     "tags": []
    },
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "e97659f2b3e241258b41f43e7407140b",
+       "model_id": "1df15f0809c94ee9b9e68b66143a2f9a",
        "version_major": 2,
        "version_minor": 0
       },
@@ -3400,7 +3400,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.11.9"
   },
   "toc": {
    "base_numbering": "3",

pyTEMlib/image_tools.py

@@ -601,8 +601,12 @@ def rigid_registration(dataset, sub_pixel=True):
     rig_reg, drift = rig_reg_drift(dataset, relative_drift)
     crop_reg, input_crop = crop_image_stack(rig_reg, drift)
 
-    rigid_registered = dataset.like_data(crop_reg)
-    rigid_registered.title = 'Rigid Registration'
+    rigid_registered = sidpy.Dataset.from_array(crop_reg, 
+                                                title='Rigid Registration', 
+                                                data_type='IMAGE_STACK',
+                                                quantity=dataset.quantity,
+                                                units=dataset.units)
+    rigid_registered.title = 'Rigid_Registration'
     rigid_registered.source = dataset.title
     rigid_registered.metadata = {'analysis': 'rigid sub-pixel registration', 'drift': drift,
                                  'input_crop': input_crop, 'input_shape': dataset.shape[1:]}
@@ -664,9 +668,9 @@ def rig_reg_drift(dset, rel_drift):
     # absolute drift
     print(rel_drift)
     drift = np.array(rel_drift).copy()
-
+    
     drift[0] = [0, 0]
-    for i in range(drift.shape[0]):
+    for i in range(1, drift.shape[0]):
         drift[i] = drift[i - 1] + rel_drift[i]
     center_drift = drift[int(drift.shape[0] / 2)]
     drift = drift - center_drift

pyTEMlib/version.py

@@ -1,6 +1,6 @@
 """
 version
 """
-_version = '0.2024.06.0'
+_version = '0.2024.08.4'
 __version__ = _version
-_time = '2024-06-10 19:58:26'
+_time = '2024-08-28 19:58:26'

setup.py

@@ -9,6 +9,7 @@
 import os
 import setuptools
 
+
 here = os.path.abspath(os.path.dirname(__file__))
 with open(os.path.join(here, 'README.rst')) as f:
     long_description = f.read()
@@ -47,7 +48,7 @@
     author="Gerd Duscher",
     author_email="[email protected]",
 
-    install_requires=['scipy', 'numpy', 'pillow',  'ase', 'tqdm', 'plotly', 'pandas', 'requests', 'lxml', 'ipympl', 
+    install_requires=['scipy', 'numpy', 'pillow',  'ase', 'tqdm', 'plotly', 'pandas', 'requests', 'lxml', 'ipympl', 'build', 
                       'spglib', 'scikit-image', 'scikit-learn', 'pyNSID>=0.0.7', 'sidpy>=0.12.1', 'SciFiReaders>=0.0.8'],  # 'PyQt5> 1.0'],#
     setup_requires=['pytest-runner'],
     tests_require=['pytest'],